Given a context passage, generate a question from the passage such that its answer is shortest continous span from the passage.

Example Input: Although peak finding in next-generation sequencing (NGS) datasets has been addressed extensively, there is no consensus on how to analyze and process biological replicates. Furthermore, most peak finders do not focus on accurate determination of enrichment site widths and are not widely applicable to different types of datasets. We developed JAMM (Joint Analysis of NGS replicates via Mixture Model clustering): a peak finder that can integrate information from biological replicates, determine enrichment site widths accurately and resolve neighboring narrow peaks. JAMM is a universal peak finder that is applicable to different types of datasets. We show that JAMM is among the best performing peak finders in terms of site detection accuracy and in terms of accurate determination of enrichment sites widths. In addition, JAMM's replicate integration improves peak spatial resolution, sorting and peak finding accuracy. JAMM is available for free and can run on Linux machines through the command line: [Link]
Example Output: Which peak calling algorithm employs mixture model clustering under the hood?

Example Input: The Bacillus anthracis toxin genes, cya, lef, and pag, can be viewed as a regulon, in which transcription of all three genes is activated in trans by the same regulatory gene, atxA, in response to the same signal, CO2. In atxA+ strains, toxin gene expression is increased 5- to 20-fold in cells grown in 5% CO2 relative to cells grown in air. CO2-enhanced toxin gene transcription is not observed in atx4-null mutants. Here, we used two independent techniques to obtain evidence for additional CO2-induced atxA-regulated genes. First, total protein preparations from atxA4+ and atxA isolates grown in 5% CO2 and in air were examined by two-dimensional electrophoresis. Comparison of the resulting protein patterns indicated that synthesis of non-toxin proteins is influenced by growth in elevated CO2 and the toxin gene regulator, atxA. Second, we generated random transcriptional lacZ fusions in B. anthracis with transposon Tn917-LTV3. Transposon-insertion libraries were screened for mutants expressing CO2-enhanced atxA-dependent beta-galactosidase activity. DNA sequence analysis of transposon insertion sites in 17 mutants carrying CO2- and atxA-regulated fusions revealed 10 mutants carrying independent insertions on the 185-kb toxin plasmid pXO1 which did not map to the toxin genes. The tcr-lacZ fusion mutants (tcr for toxin coregulated) were Tox+, indicating that these genes may not be involved in anthrax toxin gene activation. Our data indicate a clear association of atxA with CO2-enhanced gene expression in B. anthracis and provide evidence that atxA regulates genes other than the structural genes for the anthrax toxin proteins.
Example Output: Which metabolite activates AtxA?

Example Input: Bacteria are the most abundant living things on Earth. They live in almost all environments. They are found in the air, ocean, soil, and intestines of animals. They are even found in rocks deep below Earths surface. Any surface that has not been sterilized is likely to be covered with bacteria. The total number of bacteria in the world is amazing. Its estimated to be about 5 million trillion trillion. If you write that number in digits, it has 30 zeroes! Bacteria are the most diverse organisms on Earth. Thousands of species of bacteria have been discovered. Many more are thought to exist. The known species are classified on the basis of various traits. For example, they may be classified by the shape of their cells. They may also be classified by how they react to a dye called Gram stain. Bacteria come in several different shapes. The different shapes can be seen by examining bacteria under a light microscope. Therefore, its relatively easy to classify them by shape. There are three types of bacteria based on shape: bacilli (bacillus, singular), or rod shaped. cocci (coccus, singular), or sphere shaped. spirilli (spirillus, singular), or spiral shaped. You can see a common example of each type of bacteria in Figure 8.10. Different types of bacteria stain a different color when Gram stain is applied to them. This makes them easy to identify. Some stain purple and some stain red, as you can see in Figure 8.11. The two types differ in their outer layers. This explains why they stain differently. Bacteria that stain purple are called gram-positive bacteria. They have a thick cell wall without an outer membrane. Bacteria that stain red are called gram-negative bacteria. They have a thin cell wall with an outer membrane. Bacteria and people have many important relationships. Bacteria make our lives easier in a variety of ways. In fact, we could not survive without them. On the other hand, many bacteria can make us sick. Some of them are even deadly. For a dramatic overview of the many roles of bacteria, watch this stunning video: MEDIA Click image to the left or use the URL below. URL: Bacteria help usand all other living thingsby decomposing wastes. In this way, they recycle carbon and nitrogen in ecosystems. In addition, photosynthetic cyanobacteria are important producers. On ancient Earth, they added oxygen to the atmosphere and changed the course of evolution forever. There are billions of bacteria inside the human digestive tract. They help us digest food. They also make vitamins and play other important roles. We use bacteria in many other ways as well. For example, we use them to: create medical products such as vaccines. transfer genes in gene therapy. make fuels such as ethanol. clean up oil spills. kill plant pests. ferment foods. Do you eat any of the fermented foods pictured in Figure 8.12? If so, you are eating bacteria and their wastes. Yum! You have ten times as many bacterial cells as human cells in your body. Luckily for you, most of these bacteria are harmless. However, some of them can cause disease. Any organism that causes disease is called a pathogen. Diseases caused by bacterial pathogens include food poisoning, strep throat, and Lyme disease. Bacteria that cause disease may spread directly from person to person. For example, they may spread when people shake hands with, or sneeze on, other people. Bacteria may also spread through food, water, or objects that have become contaminated with them. Some bacteria are spread by vectors. A vector is an organism that spreads bacteria or other pathogens. Most vectors are animals, commonly insects. For example, deer ticks like the one in Figure 8.13 spread Lyme disease. Ticks carry Lyme disease bacteria from deer to people when they bite them. Bacteria in food or water usually can be killed by heating it to a high temperature. Generally, this temperature is at least 71 C (160 F). Bacteria on surfaces such as countertops and floors can be killed with disinfectants, such as chlorine
Example Output:
____organism that causes disease

